Brain data#

This section presents results of brain MRI data. Below are quantitative T1 values computed using the MP2RAGE and the MTsat methods. These values are averaged within the gray matter and white matter masks.

Gray matter qMRI#

Code imports#

# Python imports 
from IPython.display import clear_output
from pathlib import Path
import numpy as np
import pandas as pd

# Import custom tools
from tools.data import Data
from tools.plot import Plot

Download data#

data_type = 'brain'
release_version = 'latest'

dataset = Data(data_type)
dataset.download(release_version)
Archive:  neuromod-anat-brain-qmri.zip
  inflating: data/brain/results-neuromod-anat-brain-qmri.csv  
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  inflating: data/brain/._timeline-neuromod-anat-brain.html  
--2022-06-14 12:43:03--  https://github.com/courtois-neuromod/anat-processing/releases/download//r20210726/neuromod-anat-brain-qmri.zip
Resolving github.com (github.com)... 140.82.112.3
Connecting to github.com (github.com)|140.82.112.3|:443... connected.
HTTP request sent, awaiting response... 302 Found
Location: https://objects.githubusercontent.com/github-production-release-asset-2e65be/333825187/8209c733-4891-4342-8c30-ccd075b128f8?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20220614%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20220614T124303Z&X-Amz-Expires=300&X-Amz-Signature=79fd859211ef596844d3110ab6a53de4f6f19daa824a1ce69cd60984672f06cb&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=333825187&response-content-disposition=attachment%3B%20filename%3Dneuromod-anat-brain-qmri.zip&response-content-type=application%2Foctet-stream [following]
--2022-06-14 12:43:03--  https://objects.githubusercontent.com/github-production-release-asset-2e65be/333825187/8209c733-4891-4342-8c30-ccd075b128f8?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20220614%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20220614T124303Z&X-Amz-Expires=300&X-Amz-Signature=79fd859211ef596844d3110ab6a53de4f6f19daa824a1ce69cd60984672f06cb&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=333825187&response-content-disposition=attachment%3B%20filename%3Dneuromod-anat-brain-qmri.zip&response-content-type=application%2Foctet-stream
Resolving objects.githubusercontent.com (objects.githubusercontent.com)... 185.199.111.133, 185.199.110.133, 185.199.109.133, ...
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HTTP request sent, awaiting response... 200 OK
Length: 939721 (918K) [application/octet-stream]
Saving to: ‘neuromod-anat-brain-qmri.zip’

     0K .......... .......... .......... .......... ..........  5% 29.2M 0s
    50K .......... .......... .......... .......... .......... 10% 16.1M 0s
   100K .......... .......... .......... .......... .......... 16%  257M 0s
   150K .......... .......... .......... .......... .......... 21% 74.5M 0s
   200K .......... .......... .......... .......... .......... 27%  248M 0s
   250K .......... .......... .......... .......... .......... 32% 39.5M 0s
   300K .......... .......... .......... .......... .......... 38%  237M 0s
   350K .......... .......... .......... .......... .......... 43%  194M 0s
   400K .......... .......... .......... .......... .......... 49%  267M 0s
   450K .......... .......... .......... .......... .......... 54%  245M 0s
   500K .......... .......... .......... .......... .......... 59%  280M 0s
   550K .......... .......... .......... .......... .......... 65%  228M 0s
   600K .......... .......... .......... .......... .......... 70%  279M 0s
   650K .......... .......... .......... .......... .......... 76%  215M 0s
   700K .......... .......... .......... .......... .......... 81%  241M 0s
   750K .......... .......... .......... .......... .......... 87%  226M 0s
   800K .......... .......... .......... .......... .......... 92%  172M 0s
   850K .......... .......... .......... .......... .......... 98%  152M 0s
   900K .......... .......                                    100% 93.8M=0.01s

2022-06-14 12:43:03 (91.2 MB/s) - ‘neuromod-anat-brain-qmri.zip’ saved [939721/939721]

Load data plot it#

dataset.load()
fig_gm = Plot(dataset, plot_name = 'brain-1')

fig_gm.title = 'Brain gray matter qMRI microstructure'
# If you're running this notebook in a Jupyter Notebook (eg, on MyBinder), change 'jupyter-book' to 'notebook'
fig_gm.display('jupyter-book', tissue = 'GM')

White matter qMRI#

fig_wm = Plot(dataset, plot_name = 'brain-2')

fig_wm.title = 'Brain white matter qMRI microstructure'
# If you're running this notebook in a Jupyter Notebook (eg, on MyBinder), change 'jupyter-book' to 'notebook'
fig_wm.display('jupyter-book', tissue = 'WM')